Brand new four chromosomes found in the LD see along with displayed inversion-typical patterns throughout the PCA (Fig

Brand new four chromosomes found in the LD see along with displayed inversion-typical patterns throughout the PCA (Fig

Principle component analyses

1b, d, f, h, principle component loadings: Even more file step 1: Numbers S2–S5). The 3 autosomal inversions had several main homozygote haplotype clusters (with the heterozygous anyone in-between) together with sex chromosome split up into around three head homozygote haplotype clusters (with the heterozygous people around). The newest clusters had been well defined on autosomes but to your chromosome TguZ the least preferred haplotype (haplotype C in the Fig. 1h) appeared to enable it to be particular recombination with every of the two almost every other haplotypes, deciding to make the groups a lot more diffuse. But not, the reasonable average heterozygosity contained in this for each and every team out-of homozygotes compared in order to heterozygotes (Table 2) and average-signing up for communities (using Circle v4.six.1.step one with practical options ) with the phased SNP data during the inversion breakpoint (having fun with Beagle v3.step three.2 ; Extra file step one: Profile S6) subsequent hold the translation the LD nations portray inversion polymorphisms. It should additionally be indexed one chromosomes Tgu5 and you may TguZ had started in past times located cytogenetically to create pericentric inversions while the breakpoints meets truthfully towards the LD area limits [45, 48–50].

Regarding most recent analyses we really do not see with full confidence and this plan is ancestral and we thus label her or him considering its allele regularity (Good = biggest haplotype, B = small haplotype, C = the very least prominent haplotype for the chromosome TguZ; Fig. 1b, d, f, h; Desk dos). The big alleles of the many four inversion polymorphisms displayed surprisingly equivalent frequencies varying between 0.53 and 0.60 (Dining table 2). To your chromosome TguZ, minimum of prominent allele (haplotype C) is actually unusual (regularity 0.074; Desk 2). All the inversion polymorphisms had been inside Hardy–Weinberg harmony (HWE; Table dos) there was zero LD between the two, for example they separate by themselves (More file 2: Table S1).

Pooled heterozygosity and minor allele matters at inversion breakpoints

We calculated pooled heterozygosity (ZHp) in 50-kb non-overlapping sliding windows along each chromosome (Fig. 2a). Low values of ZHp are indicative of regions with a high degree of fixation, for example, due to positive selection ; high values of ZHp are expected, for example, in regions of local population structure (like inversions) or under balancing selection . We found pronounced peaks in ZHp at the presumed breakpoints of the inversions on chromosomes Tgu5, Tgu11, and Tgu13, whereas ZHp dropped to almost genome-wide average values in the interior of the inversions. Chromosome Tgu11 had only one such peak, suggesting that the proximal breakpoint is missing in the current genome assembly. Diversity (SNPs per site in a 50-kb window; Additional file 1: Figure S7) was slightly reduced at the presumed breakpoints of every inversion compared to the inversion’s interior (mean SNPs per site ± standard deviation at breakpoints versus interior of 0.017 ± 0.005 versus 0.020 ± 0.005 for Tgu5, 0.0057 ± 0.0036 versus 0.018 ± 0.004 for Tgu11, and 0.016 ± 0.006 versus 0.022 ± 0.004 for Tgu13; 0.021 ± 0.007 collinear autosomal genome-wide average SNPs per site). On chromosome TguZ, the entire inversion interior had high ZHp values, which only dropped to the genome-wide average outside the inverted region. Further, diversity on TguZ was markedly reduced all along the inverted region, including the presumed breakpoints, and increased to the genome-wide average only outside the inversion (0.0021 ± 0.0015 versus 0.022 ± 0.009, respectively).

a Pooled heterozygosity (ZHp) in 50-kb windows along each chromosome in the zebra finch genome. b–e For the highlighted areas in a, which are the presumed inversion breakpoints on the autosomes and the entire inversion interior on the sex chromosome, the minor allele count frequency (MAC) spectra are shown for chromosome Tgu5 with a local maximum at 0.34–0.36 and a frequency of the minor (B) haplotype in the sample of 0.35 (b), Tgu11 with a local maximum at 0.48–0.50 and a frequency of minor (B) haplotype in the sample of 0.47 (c), Tgu13 with a local maximum at 0.48–0.50 and a frequency of minor (B) haplotype in the sample of 0.50 (d), and TguZ with two local maxima at 0.28–0.30 and 0.42–0.44 and a frequency of the B haplotype in the sample of 0.30 and frequency of the major (A) haplotype in the sample of 0.63 (e). f For comparison, the MAC of all remaining SNPs peaks at an allele frequency of around 0.1 because SNPs with a lower frequency were not unambiguously called

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